Chromosome-levelde novogenome unveils the evolution ofGleditsia sinensisand thorns development

Abstract

AbstractGleditsiaLinn is widely distributed in the world andGleditsia sinensisas an important Leguminosae specie, especially its thorns, has been used in the Chinese medicine as a chief ingredient for centuries. While the lack of genome database limits its in-depth research, especially genetic regulation and molecular developmental mechanism. In this investigation, a chromosome-levelde novogenome ofG. sinensiswas assembled through PacBio HiFi, Illumina sequencing as well as those from Hi-C, genetic mapping and K-mer analysis. TheG. sinensisharbors 786.13 Mb sized genome (contig N50=1.58 Mb, scaffold N50=51.53 Mb, 2n=28) with 36, 408 protein-coding genes. The full-length transcriptome sequencing of diverse tissues was performed to assist genome functional annotation. The comparative and evolutionary analysis unveiled thatG. sinensisdiverged from the Cretaceous period approximately 76.31 million years ago (Mya) and the close relationship betweenG. sinensisand other 8 Leguminosae species. The whole-genome duplication (WGD) analysis indicatedG. sinensisunderwent three WGD events and might go through another WGD event after differentiating from other Leguminosae plants. The Weighted Gene Coexpression Network Analysis based on phenotype and differentially expressed genes further demonstrated thatGsinMYBshould be involved in the development of thorns via regulating late thorn differentiation. This investigation provides a high level genome ofGleditsiafor Leguminosae species evolution comparison and functional elucidation and also key insights for further study on the molecular regulation mechanisms of the thorns development as a special abnormal stem organ in plants and the molecular breeding ofG. sinensis.